President Asif Ali Zardari complained about the difficulties of unifying Pakistan’s fractious political parties to support a more aggressive campaign against extremists and noted it was an election year in both countries.

Reflecting the Obama administration’s mounting frustration, Mrs. Clinton told him that the only way countries have defeated insurgencies like the ones threatening Pakistan and its neighbor was by forging national unity and exercising political will.

“It’s going to take leadership,” she told a subdued Mr. Zardari, according to officials from both countries familiar with the hourlong meeting at McCormick Place last Sunday. “It’s going to take leadership from you and others.”

Mr. Zardari’s visit to the summit meeting — after an 11th-hour invitation intended as a conciliatory gesture — went well for neither the United States nor Pakistan. It not only failed to resolve a six-month deadlock over the transportation of supplies to Afghanistan, but it also underscored the poisonous distrust and political chasms in an uneasy alliance that is central to the Obama administration’s plan to end the war in Afghanistan.

“You have to look at the meeting in context of whether it’s worth the investment having Pakistan as a partner,” one Obama administration official said bitingly. The best that that official could say of Mrs. Clinton’s meeting with Mr. Zardari was that it was “not a total waste” since she was able to deliver such a pointed message.

Far from moving toward some kind of easing of tension, relations have only worsened since then. On three days last week, American drones fired missiles at what were thought to be insurgent hide-outs in northwestern Pakistan, ending a brief lull heading into the NATO summit meeting and ignoring demands by Pakistan’s Parliament to end the strikes altogether. And on Wednesday, a court in Pakistan convicted a doctor who helped the C.I.A. in the search for Osama bin Laden, sentencing him to 33 years in prison for treason.

The next day the Senate approved a new cut of $33 million in American military assistance to Pakistan, $1 million for each year of his sentence.

The failed diplomacy of the last week highlighted the inability of both countries to repair a relationship that was badly frayed by the secret raid that killed Bin Laden in May of last year and then was nearly ruptured by the NATO attack in November. It has raised questions over whether even a more limited security relationship between the two countries is even possible.

Officials from both countries expressed a desire to resolve their differences, but it appeared that both were drifting ever farther apart. “We need to scale back expectations for each other,” Sherry Rehman, Pakistan’s ambassador to the United States, said in an interview.

For Mr. Zardari, the visit to Chicago was a political disaster at home, exposing the increasingly embattled president to blistering criticism. In a clear diplomatic slight, President Obama refused to hold a meeting with him, speaking to him for only a few minutes on the way to a group photograph of the world leaders who came to Chicago to map out an end to the war in Afghanistan.

The tensions over Afghanistan, over Pakistan’s perceived unwillingness to strike against insurgents within its borders and over the continued American drone strikes have resisted a year of efforts to ease them. Mrs. Clinton has now met Mr. Zardari three times since the Bin Laden raid; after the first two she had expressed hope that the relationship was “back on track,” as she put it in Islamabad in October.

After Pakistan’s Parliament completed a review of relations with the United States in April, Mrs. Clinton and others in the State Department expected that they could reach a new understanding on security cooperation, which has been more or less delayed since November. A series of American delegations visited officials in Pakistan — led by Deputy Secretary of State Thomas R. Nides and Marc Grossman, the administration’s special envoy — only to find Pakistan changing its demands in response to domestic politics and, some said, Mr. Zardari’s weakened position.

The Pakistani Parliament demanded an unconditional apology for the November attack and an immediate end to the C.I.A. drone strikes, but it also paved the way for a reopening of NATO supply lines through Pakistan, though at a cost that the administration and members of Congress viewed as extortion.

A brazen attack on Kabul and other Afghan cities in April by the Haqqani network, Islamic militants operating from a base in Pakistan, simply hardened the administration’s stance, especially on the apology, something that also would be politically risky for Mr. Obama’s re-election campaign.

Even so, a team of American specialists remained in Islamabad to try to hammer out an agreement to reopen the supply routes. Pakistan, stung by the suspension of American military assistance last year, demanded a fee of $5,000 for each truck that crossed its territory from the port in Karachi to Afghanistan. Before the November attack, NATO had paid $250.

The Pakistanis also asked for an indemnity waiver in case American cargo is damaged, for some repairs to the port of Karachi, and for road improvements near the border crossings, the senior American official said.

Before the summit meeting in Chicago, the two sides appeared to narrow the difference, with Pakistan asking for $3,000 and the United States offering to pay up to $1,000. In hopes of finishing the deal, NATO extended a late invitation to Mr. Zardari to attend, but even the narrow issue of supply routes proved too divisive to resolve.

By the time Mrs. Clinton sat down with Mr. Zardari last Sunday, the administration had lowered its expectations. Tactically, the officials said, she pressed him to tell the NATO leaders that he was committed to resolving the dispute over the transit of supplies, which he did in a closed meeting the next day.

Most of Mr. Zardari’s meeting with Mrs. Clinton was spent on his difficulties unifying the country’s political blocs. He responded defensively. “Zardari made it clear it’s an election season where he is, and he knows it is here, too,” one administration official said.

Mrs. Clinton suggested specific ways to overcome the differences over counterterrorism operations — and to sell them to politicians in Pakistan. The officials declined to discuss those ideas, even on the condition of anonymity. The meeting ended without any clear commitments.

“The secretary,” the official said, “sought to make this very clear: Are you guys ready to move and get your whole leadership on the same page? Because sometimes it looks to us like you’re not.”

A version of this article appears in print on May 28, 2012, on page A8 of the New York edition with the headline: Frustrations Grow as U.S. and Pakistan Fail to Mend Relations. Order Reprints|Today's Paper|Subscribe